scPDB - 2fdd entry

Protein Data Bank Entry:

PDB ID : 2fdd

Resolution :1.580 Å

Experimental Method : X-ray

Deposition Date : 2005-12-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pol protein
ID:	Q7SPG9_9HIV1
AC:	Q7SPG9
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	50 %
B	50 %

Ligand binding site composition:

B-Factor:	16.152
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.963	796.500

% Hydrophobic	% Polar
44.92	55.08
According to VolSite

Ligand :

HET Code:	385
Formula:	C33H41N3O10S2
Molecular weight:	703.823 g/mol
DrugBank ID:	DB04887
Buried Surface Area:	57.39 %
Polar Surface area:	191.6 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
Rings:	6
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
16.121	13.9955	0.818917

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C34	CD2	LEU- 23	3.87	0	Hydrophobic	false
C19	CD2	LEU- 23	3.88	0	Hydrophobic	false
O18	OD1	ASP- 25	2.69	151.64	H-Bond (Protein Donor)	false
O18	OD1	ASP- 25	2.55	163.59	H-Bond (Ligand Donor)	false
N11	O	GLY- 27	3.43	157.29	H-Bond (Ligand Donor)	false
C7	CB	ALA- 28	4.12	0	Hydrophobic	false
C17	CB	ALA- 28	4.04	0	Hydrophobic	false
C38	CB	ALA- 28	3.47	0	Hydrophobic	false
C2	CB	ASP- 29	4.07	0	Hydrophobic	false
C9	CB	ASP- 29	4.32	0	Hydrophobic	false
C45	CB	ASP- 29	3.93	0	Hydrophobic	false
O6	N	ASP- 29	3.01	157.95	H-Bond (Protein Donor)	false
O5	N	ASP- 30	3.15	162.65	H-Bond (Protein Donor)	false
O44	N	ASP- 30	3.04	136.42	H-Bond (Protein Donor)	false
C40	CB	ASP- 30	4.16	0	Hydrophobic	false
C45	CB	ASP- 30	4.07	0	Hydrophobic	false
C7	CG2	VAL- 32	3.86	0	Hydrophobic	false
C38	CG2	VAL- 32	3.88	0	Hydrophobic	false
C37	CB	ILE- 47	4.36	0	Hydrophobic	false
C40	CD1	ILE- 47	4.44	0	Hydrophobic	false
C45	CG2	ILE- 47	4.01	0	Hydrophobic	false
C7	CD1	ILE- 47	4.13	0	Hydrophobic	false
C20	CG2	VAL- 50	4.4	0	Hydrophobic	false
C35	CG2	VAL- 50	3.97	0	Hydrophobic	false
C36	CG	PRO- 81	3.98	0	Hydrophobic	false
S47	CB	PRO- 81	3.81	0	Hydrophobic	false
C23	CG	PRO- 81	3.4	0	Hydrophobic	false
C34	CB	ALA- 82	3.75	0	Hydrophobic	false
C22	CB	ALA- 82	3.69	0	Hydrophobic	false
C33	CD1	ILE- 84	4.34	0	Hydrophobic	false
C35	CG1	ILE- 84	4.32	0	Hydrophobic	false
C14	CD1	ILE- 84	3.6	0	Hydrophobic	false
C34	CD1	ILE- 84	3.56	0	Hydrophobic	false